Dear R-sig phylo list members, I am trying to apply maximum Parsimony tree searches on a large number of simulated datasets within the R environment. So far I have found one function implementing Parsimony: the optim.parsimony function in the package phangorn. This function finds a shortest tree for a typical dataset (1000 taxa) reasonably fast which is great. However, the resulting tree does not include branch lengths (i.e. it is a fully bifurcating cladogram). This is problematic for me because there are nodes separating identical sequences.
Is there a way (i.e. function) to calculate branch lengths in terms of number of substitutions for a tree? ..Or does someone know an alternative function to get a maximum Parsinomy tree with branch lengths? Any help or suggestion would be most welcome. Thanks! Robin Robin van Velzen Biosystematics Group Wageningen University [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo